Publications

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2017


Associating transcription factors and conserved RNA structures with gene regulation in the human brain
Hecker N, Seemann SE, Silahtaroglu A, Ruzzo WL, Gorodkin J Scientific Reports 2017, 7(1)
[ PubMed | Paper ]

The identification and functional annotation of RNA structures conserved in vertebrates
Seemann SE, Mirza AH, Hansen C, Bang-Berthelsen CH, Garde C, Christensen-Dalsgaard M, Torarinsson E, Yao Z, Workman CT, Pociot F, Nielsen H, Tommerup N, Ruzzo WL, Gorodkin J Genome Research 2017, e-pub
[ PubMed | Paper | Dataresource | Supplement ]

Assessing the miRNA sponge potential of RUNX1T1 in t(8;21) acute myeloid leukemia
Junge A, Zandi R, Havgaard JH, Gorodkin J, Cowland JB Gene 2017, 615:35-40
[ PubMed | Paper ]

RNAscClust : clustering RNA sequences using structure conservation and graph based motifs
Miladi M, Junge A, Costa F, Seemann SE, Havgaard JH, Gorodkin J, Backofen R Bioinformatics 2017, 33(14):2089-2096
[ PubMed | Paper | Software ]

RIsearch2: suffix array-based large-scale prediction of RNA–RNA interactions and siRNA off-targets
Alkan F, Wenzel A, Palasca O, Kerpedjiev P, Rudebeck A, Stadler PF, Hofacker IL, Gorodkin J Nucleic Acids Res (2017) 45 (8): e60
[ PubMed | Paper | Software ]

RAIN: RNA–protein Association and Interaction Networks
Junge A, Refsgaard JC, Garde C, Pan X, Santos A, Alkan F, Anthon C, von Mering C, Workman CT, Jensen LJ, Gorodkin J Database 2017, 2017:baw167
[ PubMed | Paper | Webserver ]

Conference Papers


CUDA-Sankoff: Using GPU to Accelerate the Pairwise Structural RNA Alignment
Sundfeld D, Havgaard JH, Gorodkin J, Melo AC M A d 2017 25th Euromicro International Conference on Parallel, Distributed and Network-based Processing (PDP) 2017, CPAPER
[ Paper ]

2016


Joint Profiling of miRNAs and mRNAs Reveals miRNA Mediated Gene Regulation in the Göttingen Minipig Obesity Model
Mentzel CM J, Alkan F, Keinicke H, Jacobsen MJ, Gorodkin J, Fredholm M, Cirera S PLOS ONE 2016, 11(11):e0167285
[ PubMed | Paper ]

Differential transcriptional responses to Ebola and Marburg virus infection in bat and human cells
Hölzer M, Krähling V, Amman F, Barth E, Bernhart SH, Carmelo VA O, Collatz M, Doose G, Eggenhofer F, Ewald J, Fallmann J, Feldhahn LM, Fricke M, Gebauer J, Gruber AJ, Hufsky F, Indrischek H, Kanton S, Linde J, Mostajo N, Ochsenreiter R, Riege K, Rivarola-Duarte L, Sahyoun AH, Saunders SJ, Seemann SE, Tanzer A, Vogel B, Wehner S, Wolfinger MT, Backofen R, Gorodkin J, Grosse I, Hofacker I, Hoffmann S, Kaleta C, Stadler PF, Becker S, Marz M Scientific Reports 2016, 6(1)
[ PubMed | Paper ]

Quality Assessment of Domesticated Animal Genome Assemblies
Seemann S, Anthon C, Palasca O, Gorodkin J Bioinformatics and Biology Insights 2015:Suppl. 4 49-58
[ Paper ]

2015


Foldalign 2.5: multithreaded implementation for pairwise structural RNA alignment
Sundfeld D, Havgaard JH, de Melo AC M A, Gorodkin J Bioinformatics 2015, 32(8):1238-1240
[ PubMed | Paper | Webserver | Software ]

RNA 3D Modules in Genome-Wide Predictions of RNA 2D Structure
Theis C, Zirbel CL, zu Siederdissen CH, Anthon C, Hofacker IL, Nielsen H, Gorodkin J PLOS ONE 2015, 10(10):e0139900
[ PubMed | Paper ]

Full-length RNA structure prediction of the HIV-1 genome reveals a conserved core domain
Sükösd Z, Andersen ES, Seemann SE, Jensen MK, Hansen M, Gorodkin J, Kjems J Nucleic Acids Res (2015) 43 (21): 10168-10179
[ PubMed | Paper ]

Optimizing RNA structures by sequence extensions using RNAcop
Hecker N, Christensen-Dalsgaard M, Seemann SE, Havgaard JH, Stadler PF, Hofacker IL, Nielsen H, Gorodkin J Nucleic Acids Research 2015, 43(17):8135-8145
[ PubMed | Paper | Webserver | Software ]

Gender and Obesity Specific MicroRNA Expression in Adipose Tissue from Lean and Obese Pigs
Mentzel CM J, Anthon C, Jacobsen MJ, Karlskov-Mortensen P, Bruun CS, Jørgensen CB, Gorodkin J, Cirera S, Fredholm M PLOS ONE 2015, 10(7):e0131650
[ PubMed | Paper ]

Differential and coherent processing patterns from small RNAs
Pundhir S, Gorodkin J Scientific Reports 2015, 5(1)
[ PubMed | Paper | Software ]

Simultaneous DNA and RNA Mapping of Somatic Mitochondrial Mutations across Diverse Human Cancers
Stewart JB, Alaei-Mahabadi B, Sabarinathan R, Samuelsson T, Gorodkin J, Gustafsson CM, Larsson E PLOS Genetics 2015, 11(6):e1005333
[ PubMed | Paper ]

Emerging applications of read profiles towards the functional annotation of the genome
Pundhir S, Poirazi P, Gorodkin J Frontiers in Genetics 2015, 6
[ PubMed | Paper ]

Transcriptomic landscape of lncRNAs in inflammatory bowel disease
Mirza AH, Berthelsen CH, Seemann SE, Pan X, Frederiksen KS, Vilien M, Gorodkin J, Pociot F Genome Medicine 2015, 7(1)
[ PubMed | Paper ]

Popular Science


Emerging tools for RNA structure analysis in polymorphic data
Sabarinathan R, Seemann SE, Gorodkin J Biozoom 2:3, 2015
[ Paper ]

2014


Profiling of Ribose Methylations in RNA by High-Throughput Sequencing
Birkedal U, Christensen-Dalsgaard M, Krogh N, Sabarinathan R, Gorodkin J, Nielsen H Angewandte Chemie International Edition 2015, 54(2):451
[ PubMed | Paper ]

Structured RNAs and synteny regions in the pig genome
Anthon C, Tafer H, Havgaard JH, Thomsen B, Hedegaard J, Seemann SE, Pundhir S, Kehr S, Bartschat S, Nielsen M, Nielsen RO, Fredholm M, Stadler PF, Gorodkin J BMC Genomics 2014, 15(1):459
[ PubMed | Paper ]

Spatially conserved regulatory elements identified within human and mouse Cd247 gene using high-throughput sequencing data from the ENCODE project
Pundhir S, Hannibal TD, Bang-Berthelsen CH, Wegener AK, Pociot F, Holmberg D, Gorodkin J Gene 2014, 545(1):80-87
[ PubMed | Paper ]

Transcriptome-Wide Analysis of UTRs in Non-Small Cell Lung Cancer Reveals Cancer-Related Genes with SNV-Induced Changes on RNA Secondary Structure and miRNA Target Sites
Sabarinathan R, Wenzel A, Novotny P, Tang X, Kalari KR, Gorodkin J PLoS ONE 2014, 9(1):e82699
[ PubMed | Paper ]

Books, Book Chapters


Computational Approaches for Predicting Mutation Effects on RNA Structure
Sabarinathan R, Gorodkin J In Comprehensive Biomedical Physics. Anders Brahme, Vol 6. 111, Amsterdam: Elsevier, 2014
[ Chapter ]

2013


Discovery of a divergent HPIV4 from respiratory secretions using second and third generation metagenomic sequencing
Alquezar-Planas DE, Mourier T, Bruhn CA W, Hansen AJ, Vitcetz SN, Mørk S, Gorodkin J, Nielsen HA, Guo Y, Sethuraman A, Paxinos EE, Shan T, Delwart EL, Nielsen LP Scientific Reports 2013, 3(1)
[ PubMed | Paper ]

The RNAsnp web server: predicting SNP effects on local RNA secondary structure
Sabarinathan R, Tafer H, Seemann S E, Hofacker I L, Stadler P F, Gorodkin J Nucleic Acids Research 2013, 41(W1):W475-W479
[ PubMed | Paper | Webserver | Software ]

RNAsnp: Efficient Detection of Local RNA Secondary Structure Changes Induced by SNPs
Sabarinathan R, Tafer H, Seemann SE, Hofacker IL, Stadler PF, Gorodkin J human mutation 2013, 34(4): 546
[ PubMed | Paper | Software ]

Protein-driven inference of miRNA-disease associations
Mork S, Pletscher-Frankild S, Palleja Caro A, Gorodkin J, Jensen L J Bioinformatics 2013, 30(3):392-397
[ PubMed | Paper | Software | Dataresource ]

Automated identification of RNA 3D modules with discriminative power in RNA structural alignments
Theis C, Honer zu Siederdissen C, Hofacker I L, Gorodkin J Nucleic Acids Research 2013, 41(22):9999-10009
[ PubMed | Paper | Software ]

MicroRNA discovery by similarity search to a database of RNA-seq profiles
Pundhir S, Gorodkin J Frontiers in Genetics 2013, 4
[ PubMed | Paper | Webserver ]

Books, Book Chapters


De Novo Discovery of Structured ncRNA Motifs in Genomic Sequences
Ruzzo WL, Gorodkin J In RNA Sequence, Structure, and Function: Computational and Bioinformatic Methods. Gorodkin J, Ruzzo WL (Ed.), Methods in Molecular Biology 2013, GENERIC:303-318
[ PubMed | Chapter ]

RNA Structural Alignments, Part I: Sankoff-Based Approaches for Structural Alignments
Havgaard JH, Gorodkin J In RNA Sequence, Structure, and Function: Computational and Bioinformatic Methods. Gorodkin J, Ruzzo WL (Ed.), Methods in Molecular Biology 2013, GENERIC:275-290
[ PubMed | Chapter ]

Concepts and Introduction to RNA Bioinformatics
Gorodkin J, Hofacker IL, Ruzzo WL In RNA Sequence, Structure, and Function: Computational and Bioinformatic Methods. Gorodkin J, Ruzzo WL (Ed.), Methods in Molecular Biology 2013, GENERIC:1-31
[ PubMed | Chapter ]

2012


Profiling microRNAs in lung tissue from pigs infected with Actinobacillus pleuropneumoniae
Podolska A, Anthon C, Bak M, Tommerup N, Skovgaard K, Heegaard PM, Gorodkin J, Cirera S, Fredholm M BMC Genomics 2012, 13(1):459
[ PubMed | Paper ]

Transcripts with in silico predicted RNA structure are enriched everywhere in the mouse brain
Seemann SE, Sunkin SM, Hawrylycz MJ, Ruzzo WL, Gorodkin J BMC Genomics 2012, 13(1):214
[ PubMed | Paper ]

Sequence and expression analysis of gaps in human chromosome 20
Minocherhomji S, Seemann S, Mang Y, El-schich Z, Bak M, Hansen C, Papadopoulos N, Josefsen K, Nielsen H, Gorodkin J, Tommerup N, Silahtaroglu A Nucleic Acids Research 2012, 40(14):6660-6672
[ PubMed | Paper ]

Analyses of pig genomes provide insight into porcine demography and evolution
Groenen MA M, Archibald AL, Uenishi H, Tuggle CK, Takeuchi Y, Rothschild MF, Rogel-Gaillard C, Park C, Milan D, Megens H, Li S, Larkin DM, Kim H, Frantz LA F, Caccamo M, Ahn H, Aken BL, Anselmo A, Anthon C, Auvil L, Badaoui B, Beattie CW, Bendixen C, Berman D, Blecha F, Blomberg J, Bolund L, Bosse M, Botti S, Bujie Z, Bystrom M, Capitanu B, Carvalho-Silva D, Chardon P, Chen C, Cheng R, Choi S, Chow W, Clark RC, Clee C, Crooijmans RP M A, Dawson HD, Dehais P, De Sapio F, Dibbits B, Drou N, Du Z, Eversole K, Fadista J, Fairley S, Faraut T, Faulkner GJ, Fowler KE, Fredholm M, Fritz E, Gilbert JG R, Giuffra E, Gorodkin J, Griffin DK, Harrow JL, Hayward A, Howe K, Hu Z, Humphray SJ, Hunt T, Hornshøj H, Jeon J, Jern P, Jones M, Jurka J, Kanamori H, Kapetanovic R, Kim J, Kim J, Kim K, Kim T, Larson G, Lee K, Lee K, Leggett R, Lewin HA, Li Y, Liu W, Loveland JE, Lu Y, Lunney JK, Ma J, Madsen O, Mann K, Matthews L, McLaren S, Morozumi T, Murtaugh MP, Narayan J, Truong Nguyen D, Ni P, Oh S, Onteru S, Panitz F, Park E, Park H, Pascal G, Paudel Y, Perez-Enciso M, Ramirez-Gonzalez R, Reecy JM, Rodriguez-Zas S, Rohrer GA, Rund L, Sang Y, Schachtschneider K, Schraiber JG, Schwartz J, Scobie L, Scott C, Searle S, Servin B, Southey BR, Sperber G, Stadler P, Sweedler JV, Tafer H, Thomsen B, Wali R, Wang J, Wang J, White S, Xu X, Yerle M, Zhang G, Zhang J, Zhang J, Zhao S, Rogers J, Churcher C, Schook LB Nature 2012, 491(7424):393-398
[ PubMed | Paper | Dataresource ]

RIsearch: fast RNA–RNA interaction search using a simplified nearest-neighbor energy model
Wenzel A, Akbaşli E, Gorodkin J Bioinformatics 2012, 28(21):2738-2746
[ PubMed | Paper | Software ]

Multiple independent analyses reveal only transcription factors as an enriched functional class associated with microRNAs
Croft L, Szklarczyk D, Jensen L, Gorodkin J BMC Systems Biology 2012, 6(1):90
[ PubMed | Paper | Dataresource ]

RILogo: visualizing RNA–RNA interactions
Menzel P, Seemann SE, Gorodkin J Bioinformatics 2012, 28(19):2523-2526
[ PubMed | Paper | Webserver | Software ]

Books, Book Chapters


Comparative ncRNA Gene and Structure Prediction Using Foldalign and FoldalignM
Havgaard J, Kaur S, Gorodkin J Current Protocols in Bioinformatics 2012, CHAP
[ PubMed | Chapter ]

2011


deepBlockAlign: a tool for aligning RNA-seq profiles of read block patterns
Langenberger D, Pundhir S, Ekstrøm CT, Stadler PF, Hoffmann S, Gorodkin J Bioinformatics 2011, 28(1):17-24
[ PubMed | Paper | Software ]

From Structure Prediction to Genomic Screens for Novel Non-Coding RNAs
Gorodkin J, Hofacker IL PLoS Computational Biology 2011, 7(8):e1002100
[ PubMed | Paper ]

The PETfold and PETcofold web servers for intra- and intermolecular structures of multiple RNA sequences
Seemann S E, Menzel P, Backofen R, Gorodkin J Nucleic Acids Research 2011, 39(suppl):W107-W111
[ PubMed | Paper | Webserver ]

Fast local fragment chaining using sum-of-pair gap costs
Otto C, Hoffmann S, Gorodkin J, Stadler PF Algorithms for Molecular Biology 2011, 6(1):4
[ PubMed | Paper | Software ]

Global microRNA Analysis of the NCI-60 Cancer Cell Panel
Sokilde R, Kaczkowski B, Podolska A, Cirera S, Gorodkin J, Moller S, Litman T Molecular Cancer Therapeutics 2011, 10(3):375-384
[ PubMed | Paper ]

2010


maxAlike: maximum likelihood-based sequence reconstruction with application to improved primer design for unknown sequences
Menzel P, Stadler PF, Gorodkin J Bioinformatics 2010, 27(3):317-325
[ PubMed | Paper | Webserver | Software ]

PETcofold: predicting conserved interactions and structures of two multiple alignments of RNA sequences
Seemann SE, Richter AS, Gesell T, Backofen R, Gorodkin J Bioinformatics 2010, 27(2):211-219
[ PubMed | Paper | Webserver | Software ]

Hierarchical folding of multiple sequence alignments for the prediction of structures and RNA-RNA interactions
Seemann SE, Richter AS, Gorodkin J, Backofen R Algorithms for Molecular Biology 2010, 5(1):22
[ PubMed | Paper ]

A study of alternative splicing in the pig
Nygard A, Cirera S, Gilchrist MJ, Gorodkin J, Jørgensen CB, Fredholm M BMC Research Notes 2010, 3(1):123
[ PubMed | Paper | Dataresource ]

De novo prediction of structured RNAs from genomic sequences
Gorodkin J, Hofacker IL, Torarinsson E, Yao Z, Havgaard JH, Ruzzo WL Trends in Biotechnology 2010, 28(1):9-19
[ PubMed | Paper | Dataresource | Sup ]

Books, Book Chapters


Evolutionary Genomics of MicroRNAs and Their Relatives
Tanzer A, Riester M, Hertel J, Bermudez-Santana CI, Gorodkin J, Hofacker IL, Stadler PF In Evolutionary Genomics and Systems Biology. Gustavo Caetano-Anolles (Ed.), Wiley-Blackwell, Hoboken NJ, 2010, pp. 295-327.
[ Paper | Abstract ]

2009


454 pyrosequencing based transcriptome analysis of Zygaena filipendulae with focus on genes involved in biosynthesis of cyanogenic glucosides
Zagrobelny M, Scheibye-Alsing K, Jensen N, Møller B, Gorodkin J, Bak S BMC Genomics 2009, 10(1):574
[ PubMed | Paper ]

The tedious task of finding homologous noncoding RNA genes
Menzel P, Gorodkin J, Stadler P F RNA 2009, 15(12):2075-2082
[ PubMed | Paper | Dataresource | Sup ]

Sequence assembly
Scheibye-Alsing K, Hoffmann S, Frankel A, Jensen P, Stadler P, Mang Y, Tommerup N, Gilchrist M, Nygård A, Cirera S, Jørgensen C, Fredholm M, Gorodkin J Computational Biology and Chemistry 2009, 33(2):121-136
[ PubMed | Paper | Dataresource | Sup ]

Conference Papers


Maximum Likelihood Estimation of Weight Matrices for Targeted Homology Search
Menzel P, Gorodkin J, Stadler PF Lecture Notes in Informatics: Proceedings of the German Conference on Bioinformatics. 212-220, 2009
[ Paper | Abstract ]

2008


Unifying evolutionary and thermodynamic information for RNA folding of multiple alignments
Seemann SE, Gorodkin J, Backofen R Nucleic Acids Research 2008, 36(20):6355-6362
[ PubMed | Paper | Sup ]

SNP-finding in pig mitochondrial ESTs
Scheibye-Alsing K, Cirera S, Gilchrist M J, Fredholm M, Gorodkin J Animal Genetics 2008, 39(2):193-195
[ PubMed | Paper ]

Comparative genomics beyond sequence-based alignments: RNA structures in the ENCODE regions
Torarinsson E, Yao Z, Wiklund E D, Bramsen J B, Hansen C, Kjems J, Tommerup N, Ruzzo W L, Gorodkin J Genome Research 2008, 18(2):242-251
[ PubMed | Paper | Dataresource | Sup ]

Structural profiles of human miRNA families from pairwise clustering
Kaczkowski B, Torarinsson E, Reiche K, Havgaard J H, Stadler P F, Gorodkin J Bioinformatics 2008, 25(3):291-294
[ PubMed | Paper | Dataresource | Sup ]

2007


Fast Pairwise Structural RNA Alignments by Pruning of the Dynamical Programming Matrix
Havgaard JH, Torarinsson E, Gorodkin J PLoS Computational Biology 2007, 3(10):e193
[ PubMed | Paper | Software | Sup ]

EST analysis on pig mitochondria reveal novel expression differences between developmental and adult tissues
Scheibye-Alsing K, Cirera S, Gilchrist MJ, Fredholm M, Gorodkin J BMC Genomics 2007, 8(1):367
[ PubMed | Paper |Sup1 Sup2 Sup3 ]

Detection of RNA structures in porcine EST data and related mammals
Seemann SE, Gilchrist MJ, Hofacker IL, Stadler PF, Gorodkin J BMC Genomics 2007, 8(1):316
[ PubMed | Paper |Sup1 Sup2 ]

Semiautomated improvement of RNA alignments
Andersen E S, Lind-Thomsen A, Knudsen B, Kristensen S E, Havgaard J H, Torarinsson E, Larsen N, Zwieb C, Sestoft P, Kjems J, Gorodkin J RNA 2007, 13(11):1850-1859
[ PubMed | Paper | Software | Sup ]

Identification of 10 882 porcine microsatellite sequences and virtual mapping of 4528 of these sequences
Karlskov-Mortensen P, Hu Z L, Gorodkin J, Reecy J M, Fredholm M Animal Genetics 2007, 38(4):401-405
[ PubMed | Paper | Sup ]

Principles and Limitations of Computational MicroRNA Gene and Target Finding
Lindow M, Gorodkin J DNA and Cell Biology 2007, 26(5):339-351
[ PubMed | Paper | Sup ]

Porcine transcriptome analysis based on 97 non-normalized cDNA libraries and assembly of 1,021,891 expressed sequence tags
Gorodkin J, Cirera S, Hedegaard J, Gilchrist MJ, Panitz F, Jørgensen C, Scheibye-Knudsen K, Arvin T, Lumholdt S, Sawera M, Green T, Nielsen BJ, Havgaard JH, Rosenkilde C, Wang J, Li H, Li R, Liu B, Hu S, Dong W, Li W, Yu J, Wang J, Stærfeldt H, Wernersson R, Madsen LB, Thomsen B, Hornshøj H, Bujie Z, Wang X, Wang X, Bolund L, Brunak S, Yang H, Bendixen C, Fredholm M Genome Biology 2007, 8(4):R45
[ PubMed | Paper | Dataresource |Sup1 Sup2 Sup3 Sup4 ]

Multiple structural alignment and clustering of RNA sequences
Torarinsson E, Havgaard J H, Gorodkin J Bioinformatics 2007, 23(8):926-932
[ PubMed | Paper ]

Conference Papers


SNP mining porcine ESTs with MAVIANT, a novel tool for SNP evaluation and annotation
Panitz F, Stengaard H, Hornshoj H, Gorodkin J, Hedegaard J, Cirera S, Thomsen B, Madsen L B, Hoj A, Vingborg R K, Zahn B, Wang X, Wang X, Wernersson R, Jorgensen C B, Scheibye-Knudsen K, Arvin T, Lumholdt S, Sawera M, Green T, Nielsen B J, Havgaard J H, Brunak S, Fredholm M, Bendixen C Bioinformatics 2007, 23(13):i387-i391
[ PubMed | Paper ]

2006


MicroRNA sequence motifs reveal asymmetry between the stem arms
Gorodkin J, Havgaard J, Ensterö M, Sawera M, Jensen P, Öhman M, Fredholm M Computational Biology and Chemistry 2006, 30(4):249-254
[ PubMed | Paper | Sup ]

Linkage mapping of gene-associated SNPs to pig chromosome 11
Sawera M, Cirera S, Jorgensen C B, Gorodkin J, Fredholm M Animal Genetics 2006, 37(3):199-204
[ PubMed | Paper ]

2005


Mapping and expression studies of the mir17-92 cluster on pig Chromosome 11
Sawera M, Gorodkin J, Cirera S, Fredholm M Mammalian Genome 2005, 16(8):594-598
[ PubMed | Paper ]

A high-resolution comparative map between pig chromosome 17 and human chromosomes 4, 8, and 20: Identification of synteny breakpoints
Lahbib-Mansais Y, Karlskov-Mortensen P, Mompart F, Milan D, Jørgensen CB, Cirera S, Gorodkin J, Faraut T, Yerle M, Fredholm M Genomics 2005, 86(4):405-413
[ PubMed | Paper ]

The FOLDALIGN web server for pairwise structural RNA alignment and mutual motif search
Havgaard J H, Lyngso R B, Gorodkin J Nucleic Acids Research 2005, 33(Web Server):W650-W653
[ PubMed | Paper | Webserver | Software | Sup ]

Pigs in sequence space: a 0.66X coverage pig genome survey based on shotgun sequencing
Wernersson R, Schierup MH, Jørgensen FG, Gorodkin J, Panitz F, Stærfeldt H, Christensen OF, Mailund T, Hornshøj H, Klein A, Wang J, Liu B, Hu S, Dong W, Li W, Wong GK, Yu J, Wang J, Bendixen C, Fredholm M, Brunak S, Yang H, Bolund L BMC Genomics 2005, 6(1):70
[ PubMed | Paper | Dataresource |Sup1 Sup2 ]

Pairwise local structural alignment of RNA sequences with sequence similarity less than 40%
Havgaard J H, Lyngso R B, Stormo G D, Gorodkin J Bioinformatics 2005, 21(9):1815-1824
[ PubMed | Paper ]

2004


Comparing two K-category assignments by a K-category correlation coefficient
Gorodkin J Computational Biology and Chemistry 2004, 28(5-6):367-374
[ PubMed | Paper | Webserver | Software ]

Evolutionary rate variation and RNA secondary structure prediction
Knudsen B, Andersen E, Damgaard C, Kjems J, Gorodkin J Computational Biology and Chemistry 2004, 28(3):219-226
[ PubMed | Paper ]

RNA interactions in the 5' region of the HIV-1 genome
Damgaard CK, Andersen ES, Knudsen B, Gorodkin J, Kjems J J Mol Biol. 336:369-79, 2004
[ PubMed | Paper ]

2003


tmRDB (tmRNA database)
Zwieb C, Gorodkin J, Knudsen B, Burks J, Wower J Nucleic Acids Res. 31:446-7, 2003
[ PubMed | Paper | Database ]

SRPDB: Signal Recognition Particle Database
Rosenblad MA, Gorodkin J, Knudsen B, Zwieb C, Samuelsson T Nucleic Acids Res. 31:363-4, 2003
[ PubMed | Paper | Database ]

2001


A mini-greedy algorithm for faster structural RNA stem-loop search
Gorodkin J, Lyngso RB, Stormo GD Genome Inform. 12:184-93, 2001
[ PubMed | Paper ]

Semi-automated update and cleanup of structural RNA alignment databases
Gorodkin J, Zwieb C, Knudsen B Bioinformatics. 17:642-5, 2001
[ PubMed | Paper | Webserver | Software ]

Discovering common stem-loop motifs in unaligned RNA sequences
Gorodkin J, Stricklin SL, Stormo GD Nucleic Acids Res. 29:2135-44, 2001
[ PubMed | Paper ]

Recognition of environmental and genetic effects on barley phenolic fingerprints by neural networks
Gorodkin J, Sogaard B, Bay H, Doll H, Kolster P, Brunak S Comput Chem. 25:301-7, 2001
[ PubMed | Paper ]

tmRDB (tmRNA database)
Knudsen B, Wower J, Zwieb C, Gorodkin J Nucleic Acids Res. 29:171-2, 2001
[ PubMed | Paper ]

SRPDB (Signal Recognition Particle Database)
Gorodkin J, Knudsen B, Zwieb C, Samuelsson T Nucleic Acids Res. 29:169-70, 2001
[ PubMed | Paper ]

1999


MatrixPlot: visualizing sequence constraints
Gorodkin J, Staerfeldt HH, Lund O, Brunak S Bioinformatics. 15:769-70, 1999
[ PubMed | Paper | Webserver | Software ]

Conference Papers


Using sequence motifs for enhanced neural network prediction of protein distance constraints
Gorodkin J, Lund O, Andersen CA, Brunak S Proc Int Conf Intell Syst Mol Biol. 1999:95-105.
[ PubMed | Paper ]

1998


Computational applications of DNA structural scales
Baldi P, Chauvin Y, Brunak S, Gorodkin J, Pedersen AG Proc Int Conf Intell Syst Mol Biol. 6:35-42, 1998
[ PubMed | Paper ]

1997


Universal distribution of saliencies for pruning in layered neural networks
Gorodkin J, Hansen LK, Lautrup B, Solla SA Int J Neural Syst. 1997 Oct-Dec;8(5-6):489-98.
[ PubMed | Paper ]

Protein distance constraints predicted by neural networks and probability density functions
Lund O, Frimand K, Gorodkin J, Bohr H, Bohr J, Hansen J, Brunak S Protein Eng. 10:1241-8, 1997
[ PubMed | Paper | Oldserver ]

Displaying the information contents of structural RNA alignments: the structure logos
Gorodkin J, Heyer LJ, Brunak S, Stormo GD Comput Appl Biosci. 13:583-6, 1997
[ PubMed | Paper | Webserver ]

Finding the most significant common sequence and structure motifs in a set of RNA sequences
Gorodkin J, Heyer LJ, Stormo GD Nucleic Acids Res. 25:3724-32, 1997
[ PubMed | Paper ]

Orbits of Boolean functions
Gorodkin J Discrete Applied Mathematics 75, 269-275, 1997
[ Paper | Abstract ]

Conference Papers


Finding common sequence and structure motifs in a set of RNA sequences
Gorodkin J, Heyer LJ, Stormo GD Proc Int Conf Intell Syst Mol Biol. 5:120-3, 1997
[ PubMed | Paper ]

1993


A quantitative study of pruning by optimal brain damage
Gorodkin J, Hansen LK, Krogh A, Svarer C, Winther O Int J Neural Syst. 4:159-69, 1993
[ PubMed | Paper ]

Neural Networks and Cellular Automata Complexity
Gorodkin J, Sorensen A, Winther O Complex Systems 7, 1-23, 1993
[ Paper | Abstract ]